domain_mapping — domain_mapping • browseMetadata

This function will read in the metadata file for a chosen dataset, loop through all the data elements, and ask the user to catergorise/label each data element as belonging to one or more domains.

The domains will appear in the Plots tab and dataset information will be printed to the R console, for the user's reference in making these categorisations.

These categorisations will be saved to a csv file, alongside a log file which summarises the session details. To speed up this process, some auto-categorisations will be made by the function for commonly occurring data elements and categorisations for the same data element can be copied from one table to another.

Example inputs are provided within the package data, for the user to run this function in a demo mode.

Usage

domain_mapping(
  json_file = NULL,
  domain_file = NULL,
  look_up_file = NULL,
  output_dir = NULL,
  table_copy = TRUE
)

Arguments

json_file: The metadata file. This should be downloaded from the metadata catalogue as a json file. See 'data-raw/maternity_indicators_dataset_(mids)_20240105T132210.json' for an example download.
domain_file: The domain list file. This should be a csv file created by the user, with each domain listed on a separate line. See 'data-raw/domain_list_demo.csv' for a template.
look_up_file: The look-up table file, with auto-categorisations. By default, the code uses 'data/look-up.rda'. The user can provide their own look-up table in the same format as 'data-raw/look-up.csv'.
output_dir: The path to the directory where the two csv output files will be saved. By default, the current working directory is used.
table_copy: Turn on copying between tables (TRUE or FALSE, default TRUE). If TRUE, categorisations you made for all other tables in this dataset will be copied over (if 'OUTPUT_' files are found in output_dir).

Value

The function will return two csv files: 'OUTPUT_' which contains the mappings and 'LOG_' which contains details about the dataset and session.

Examples

# Run in demo mode by providing no inputs: domain_mapping()
# Demo mode will use the /data files provided in this package
# For more guidance, refer to the package README.md file and the R manual files.